Many models of common human diseases and numerous traits of great biological interest vary among inbred strains of laboratory mice. Dissecting their multigenic control and identifying the responsible genes has been notoriously difficult. Chromosome substitution strains (CSSs), single chromosome substitutions on a defined and inbred genetic background, represent a novel and powerful paradigm. Proof-of-concept studies, with funds from other sources, demonstrated that these strains are remarkably powerful for detecting genetic variants that eluded detection with any other mapping method. During the previous funding period, we completed construction of the 22 CSSs in the B6.A-Chr panel. These strains were provided to the Jackson Laboratory for preservation and distribution as a resource for the biomedical research community. In addition, one A.B6-Chr CSS, and eight 129.B6 and B6.129 CSSs were completed and the remainder of these panels is under construction. We propose two Specific Aims: Specific Aim 1: Complete construction of the 129.B6 and B6.129 CSSs. Eight strains are complete and the remainder is at various stages of backcrossing. These CSSs can be used to dissect the genetic control of traits that differ between these strains, they can be used to characterize modifier genes that modulate phenotypes of mice with engineered mutations that are made with ES (embryonic stem) cells that are derived from 129/Sv mice, and they can be used to identify proteins that are critical to establish ES cell lines. Specific Aim 2: Complete construction of 10 129.MOLF CSSs. These strains will be valuable for studying traits that differ between these strains that are derived from mice that diverged more than 100,000 years ago. These strains can also be used to characterize modifier genes that modulate phenotypes in these mice. These CSS panels will revolutionize studies of complex traits by facilitating detection and discovery of QTLs.